Reconstruction of late Quaternary sea level history in areas of glacioisostatic uplift often relies on sediment archives from coastal isolation basins, natural coastal rock depressions previously isolated from or connected to the sea at different times. Proxy indicators for marine, brackish, or lacustrine conditions combined with precise dating can constrain the time when the sea crossed the sill threshold and isolated (or connected) the basin. The utility of isolation basins in investigations of sea level change is well known, but investigations have been mostly limited to microfossil proxies, the application of which can be limited by preservation and nonanalog problems. Here we investigate the potential of long-chain alkenones, alkenoates, and bulk organic parameters (TOC, Corg/N) for reconstructing past sea level changes in isolation basins in NW Scotland. We analyze organic biomarkers and bulk parameters from both modern basins (at different stages of isolation from the sea) and fossil basins (with sea level histories reconstructed from established proxies). Logit regression analysis was employed to find which of the biomarker metrics or bulk organic measurements could reliably characterize the sediment samples in terms of a marine/brackish or isolated/lacustrine origin. The results suggested a good efficiency for the alkenone index %C37:4 at predicting the depositional origin of the sediments. This study suggests that alkenones could be used as a novel proxy for sea level change in fossil isolation basins especially when microfossil preservation is poor.